In [ ]:
#Hide warnings on the notebook
import warnings
warnings.filterwarnings('ignore')

0. Import Packges¶

In [ ]:
from TaxaFuncExplore.taxaFuncAnalyzer import TaxaFuncAnalyzer
from TaxaFuncExplore.taxaFuncPloter.basic_plot import BasicPlot
from TaxaFuncExplore.taxaFuncPloter.heatmap_plot import HeatmapPlot
from TaxaFuncExplore.taxaFuncPloter.volcano_plot import VolcanoPlot
from TaxaFuncExplore.taxaFuncPloter.tukey_plot import TukeyPlot
from TaxaFuncExplore.taxaFuncPloter.line_plot import LinePlot
from TaxaFuncExplore.taxaFuncPloter.sankey_plot import SankeyPlot

1. Create an instance of TaxaFuncAnalyzer¶

  • Set the path of pep2taxafunc and meta tables
In [ ]:
meta_path = 'tests/Sweetener_Meta.txt'
df_path = 'tests/sw.tsv'

sw = TaxaFuncAnalyzer(df_path, meta_path)
In [ ]:
display(sw.original_df.head(5))
display(sw.meta_df.head(5))
Sequence Proteins V1_01 V1_02 V1_03 V1_04 V1_05 V1_06 V1_07 V1_08 ... Preferred_name Preferred_name_prop GOs GOs_prop KEGG_ko KEGG_ko_prop KEGG_Pathway KEGG_Pathway_prop PFAMs PFAMs_prop
0 (AccQTag)DGPMPQTNEHVLLAR MGYG000004756_01173 0 0 0 315416 0 0 0 143071 ... tuf 1.0 unknown 1.0 ko:K02358 1.0 unknown 1.0 GTP_EFTU,GTP_EFTU_D2,GTP_EFTU_D3 1.0
1 (AccQTag)QPVENAVVLGVVAELAK MGYG000002517_02511 0 0 0 0 0 0 0 0 ... unknown 1.0 unknown 1.0 ko:K03406 1.0 ko02020,ko02030,map02020,map02030 1.0 4HB_MCP_1,MCPsignal,dCache_1 1.0
2 (Acetyl)AAVDATAVSPEELQAK MGYG000003683_00301;MGYG000001490_01143 422996 780124 1091422 984615 593835 1093220 600823 861960 ... pflB 1.0 unknown 1.0 ko:K00656 1.0 ko00620,ko00640,ko00650,ko01100,ko01120,map006... 1.0 Bac_luciferase,Fer4_12,Gly_radical,PFL-like,Ra... 1.0
3 (Acetyl)ADADIASDDAIKK MGYG000000212_00409 0 867943 0 0 0 0 0 0 ... unknown 1.0 unknown 1.0 unknown 1.0 unknown 1.0 Peripla_BP_4 1.0
4 (Acetyl)ADQLTEEQIAEFK sp|P0DP24|CALM2_HUMAN;sp|P0DP25|CALM3_HUMAN;sp... 0 0 0 0 0 0 0 0 ... unknown 1.0 unknown 1.0 unknown 1.0 unknown 1.0 unknown 1.0

5 rows × 213 columns

Sample Person Treatment Sweetener Sweetener_detail
0 V1_01 V1 PBS PBS PBSB
1 V1_02 V1 Treatment ISO ISO
2 V1_03 V1 Treatment SOR SORC
3 V1_04 V1 Treatment ERY ERY
4 V1_05 V1 Treatment HSH HSH

1.1 Set function, taxon level and meta colunms for analysis¶

  • Set function for downstream analysis
  • Set taxon level for downstream analysis
  • which cols as group (If the meta table contains multiple grouping methods)
In [ ]:
sw.set_func('Description')
sw.set_multi_tables(level='s')
sw.set_group('Sweetener')

Function number: 4276
Taxa number: 1194
Taxa-Function number: 20739
group is set to Sweetener
 {'XYL', 'NDC', 'ADV', 'STE', 'SAC05', 'BAS', 'MAN', 'NEO006', 'REB', 'SOR', 'CYC', 'HSH', 'SAC2', 'ERY', 'NEO2', 'SAA', 'PBS', 'KES', 'ISO', 'ACE005', 'MFE', 'LAC', 'THA2', 'SUC', 'MAL', 'ACE2', 'FOS', 'GLU', 'ASP', 'THA03'}

If an error is entered, the program will give a prompt.

In [ ]:
sw.set_func('abc')

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[52], line 1
----> 1 sw.set_func('abc')

File c:\Users\Qing\OneDrive - University of Ottawa\code\TaxaFunc\TaxaFuncExplore\TaxaFuncExplore\taxaFuncAnalyzer.py:43, in TaxaFuncAnalyzer.set_func(self, func)
     40 check_list = ['Description', 'eggNOG_OGs', 'COG_category',
     41               'Preferred_name', 'GOs', 'KEGG_ko', 'KEGG_Pathway', 'PFAMs']
     42 if func not in check_list:
---> 43     raise ValueError(f'func must be in {check_list}')
     44 else:
     45     self.func = func

ValueError: func must be in ['Description', 'eggNOG_OGs', 'COG_category', 'Preferred_name', 'GOs', 'KEGG_ko', 'KEGG_Pathway', 'PFAMs']

2. Basic stastiscal and plot¶

  • calculates the number of peptides in each taxonomic group
In [ ]:
sw.get_stats_peptide_num_in_taxa()
Out[ ]:
LCA_level count freq label
0 unknown 3559 1.98 unknown (1.98%)
1 l 9110 5.06 l (5.06%)
2 d 25437 14.12 d (14.12%)
3 p 1202 0.67 p (0.67%)
4 c 5532 3.07 c (3.07%)
5 o 7907 4.39 o (4.39%)
6 f 23773 13.20 f (13.2%)
7 g 36299 20.15 g (20.15%)
8 s 67295 37.36 s (37.36%)
In [ ]:
bp = BasicPlot(sw)
bp.plot_taxa_stats()
  • Calculating the number of species classification
In [ ]:
sw.get_stats_taxa_level()
Out[ ]:
taxa_level count
0 d 2
1 p 21
2 c 26
3 o 70
4 f 159
5 g 630
6 s 1194
In [ ]:
bp.plot_taxa_number()
  • Calculate the number and distribution of the selected functional proportion.
In [ ]:
sw.get_stats_func_prop()
Out[ ]:
prop n freq label
0 0-0.1 1452 0.81 0-0.1 (0.81%)
1 0-0.2 5798 3.22 0-0.2 (3.22%)
2 0-0.3 5383 2.99 0-0.3 (2.99%)
3 0-0.4 4416 2.45 0-0.4 (2.45%)
4 0-0.5 3194 1.77 0-0.5 (1.77%)
5 0.5-0.6 9272 5.15 0.5-0.6 (5.15%)
6 0.6-0.7 6592 3.66 0.6-0.7 (3.66%)
7 0.7-0.8 4191 2.33 0.7-0.8 (2.33%)
8 0.8-0.9 4607 2.56 0.8-0.9 (2.56%)
9 0.9-1 2932 1.63 0.9-1 (1.63%)
10 1 132277 73.44 1 (73.44%)
In [ ]:
bp.plot_prop_stats()
  • Plot PCA of a table (function, taxa or taxa-func)
  • show_label: Whether to show text labels for each point
In [ ]:
bp.plot_pca_sns(sw.func_df, 'Description', show_label=False)
Out[ ]:
<Axes: title={'center': 'PCA of Description (total variance explained: 55.61%)'}, xlabel='PC1 (40.56%)', ylabel='PC2 (15.05%)'>

3. Difference Analysis¶

3.1 ANOVA TEST¶

  • Calculate ANOVA for all groups
In [ ]:
df_anova = sw.get_stats_anova()
  • Display the ANOVA result sorted by P-value
In [ ]:
display(df_anova.sort_values(by='P-value'))
P-value f-statistic V1_14 V2_14 V3_14 V4_14 V5_14 V1_34 V2_34 V3_34 ... V1_19 V2_19 V3_19 V4_19 V5_19 V1_29 V2_29 V3_29 V4_29 V5_29
Taxon Description
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eubacterium_I|s__Eubacterium_I ramulus_A Putative cyclase 1.069379e-59 41.000241 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A Alpha amylase catalytic 2.874864e-40 20.587759 2261304 2201322 4819914 4308406 4099658 2653869 4015319 5378878 ... 4645589 3355361 6394572 3471225 3120889 2936049 2935611 6664403 6525077 5417808
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Oscillospirales|f__Ruminococcaceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii_G Synthesizes alpha-1,4-glucan chains using ADP-glucose 7.839772e-40 20.247267 2161583 1171388 1452533 547840 1226974 1436976 1340803 1374738 ... 2287953 907358 1039238 505004 564216 1998224 481404 1342607 643314 941314
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Oscillospirales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii Putative cyclase 7.169301e-36 17.336740 0 0 0 574450 245255 240240 0 131981 ... 0 0 0 0 0 475270 358287 366993 829588 1802211
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A sp003477525 Alpha amylase catalytic 1.162862e-35 17.191300 752058 501677 338422 406385 0 257363 573499 560082 ... 637378 454122 600596 200481 0 305700 1161917 220976 760564 255284
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
d__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__UBA7173|s__UBA7173 sp900548705 Restriction endonuclease EcoRII, N-terminal 1.000000e+00 0.055804 9622497 0 0 0 0 9372924 0 0 ... 6855554 0 0 0 0 9056019 0 0 0 0
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Oscillospirales|f__Ruminococcaceae|g__Gemmiger|s__Gemmiger sp900540775 Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors 1.000000e+00 0.052012 795406 0 0 0 0 849258 0 0 ... 736983 0 0 0 0 1166248 0 0 0 0
d__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes_A|s__Alistipes_A sp900546005 Dihydrolipoyl dehydrogenase 1.000000e+00 0.048783 821596 0 0 0 0 756031 0 0 ... 694901 0 0 0 0 628216 0 0 0 198233
d__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sp002493165 TonB-linked outer membrane protein, SusC RagA family 1.000000e+00 0.045900 165038 27105959 935682 1009706 2765160 1128890 17026504 960438 ... 620187 19409901 533998 1960642 1609337 0 26000938 358024 361038 1921853
d__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei nuclear chromosome segregation 1.000000e+00 0.021218 1295530 2616270 44453652 2191325 0 2186680 3029660 29475129 ... 2859969 3078600 43086120 666617 367647 2068236 1483282 36460724 5979153 1458923

20739 rows × 192 columns

  • plot taxa-function across heatmap

Top 200, f-statistical, fig size: 30*30

In [ ]:
hp = HeatmapPlot(sw)
hp.plot_top_taxa_func_heatmap_of_test_res(df_anova, sw.func, 200, 'f', (30,30))

Table size: 20739 x 192
Recommended figure size: width: 40, length: 40, front_title: 20, font_size: 10
Out[ ]:
<seaborn.matrix.ClusterGrid at 0x18781a360d0>

Top 100, p-value, auto figsize

In [ ]:
hp.plot_top_taxa_func_heatmap_of_test_res(df_anova, sw.func, 100, 'p')

Table size: 20739 x 192
Recommended figure size: width: 40, length: 40, front_title: 20, font_size: 10
Out[ ]:
<seaborn.matrix.ClusterGrid at 0x187818ecdc0>

3.2 TUKEY TEST¶

  • Select species and functions of interest for TUKEY testing
In [ ]:
taxon = 'd__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A'
function = 'Alpha amylase catalytic'
df_tukey = sw.get_stats_tukey_test(taxon_name=taxon, func_name=function)

          Multiple Comparison of Means - Tukey HSD, FWER=0.05           
========================================================================
group1 group2    meandiff    p-adj      lower          upper      reject
------------------------------------------------------------------------
ACE005   ACE2       102736.2    1.0  -9580060.2742   9785532.6742  False
ACE005    ADV       497062.0    1.0  -9185734.4742  10179858.4742  False
ACE005    ASP      1149026.0    1.0  -8533770.4742  10831822.4742  False
ACE005    BAS   -292064.5333    1.0  -8198034.7483   7613905.6816  False
ACE005    CYC       601164.2    1.0  -9081632.2742  10283960.6742  False
ACE005    ERY      1392532.2    1.0  -8290264.2742  11075328.6742  False
ACE005    FOS      1317520.4    1.0  -8365276.0742  11000316.8742  False
ACE005    GLU      1976288.8    1.0  -7706507.6742  11659085.2742  False
ACE005    HSH     10672654.0 0.0134    989857.5258  20355450.4742   True
ACE005    ISO     28356890.8    0.0  18674094.3258  38039687.2742   True
ACE005    KES       934088.2    1.0  -8748708.2742  10616884.6742  False
ACE005    LAC       399020.4    1.0  -9283776.0742  10081816.8742  False
ACE005    MAL     34525732.0    0.0  24842935.5258  44208528.4742   True
ACE005    MAN       453252.2    1.0   -7452718.015    8359222.415  False
ACE005    MFE      -753228.2    1.0 -10436024.6742   8929568.2742  False
ACE005    NDC        58992.8    1.0  -9623803.6742   9741789.2742  False
ACE005 NEO006       143415.6    1.0  -9539380.8742   9826212.0742  False
ACE005   NEO2       333360.4    1.0  -9349436.0742  10016156.8742  False
ACE005    PBS    331933.6667    1.0  -7574036.5483   8237903.8816  False
ACE005    REB        18206.0    1.0  -9664590.4742   9701002.4742  False
ACE005    SAA      1431723.2    1.0  -8251073.2742  11114519.6742  False
ACE005  SAC05      -151109.6    1.0  -9833906.0742   9531686.8742  False
ACE005   SAC2        82987.6    1.0  -9599808.8742   9765784.0742  False
ACE005    SOR    743623.9333    1.0  -7162346.2816   8649594.1483  False
ACE005    STE      -587363.6    1.0 -10270160.0742   9095432.8742  False
ACE005    SUC       594158.2    1.0  -9088638.2742  10276954.6742  False
ACE005  THA03       555801.4    1.0  -9126995.0742  10238597.8742  False
ACE005   THA2       659406.4    1.0  -9023390.0742  10342202.8742  False
ACE005    XYL      1357668.8    1.0  -8325127.6742  11040465.2742  False
  ACE2    ADV       394325.8    1.0  -9288470.6742  10077122.2742  False
  ACE2    ASP      1046289.8    1.0  -8636506.6742  10729086.2742  False
  ACE2    BAS   -394800.7333    1.0  -8300770.9483   7511169.4816  False
  ACE2    CYC       498428.0    1.0  -9184368.4742  10181224.4742  False
  ACE2    ERY      1289796.0    1.0  -8393000.4742  10972592.4742  False
  ACE2    FOS      1214784.2    1.0  -8468012.2742  10897580.6742  False
  ACE2    GLU      1873552.6    1.0  -7809243.8742  11556349.0742  False
  ACE2    HSH     10569917.8 0.0154    887121.3258  20252714.2742   True
  ACE2    ISO     28254154.6    0.0  18571358.1258  37936951.0742   True
  ACE2    KES       831352.0    1.0  -8851444.4742  10514148.4742  False
  ACE2    LAC       296284.2    1.0  -9386512.2742   9979080.6742  False
  ACE2    MAL     34422995.8    0.0  24740199.3258  44105792.2742   True
  ACE2    MAN       350516.0    1.0   -7555454.215    8256486.215  False
  ACE2    MFE      -855964.4    1.0 -10538760.8742   8826832.0742  False
  ACE2    NDC       -43743.4    1.0  -9726539.8742   9639053.0742  False
  ACE2 NEO006        40679.4    1.0  -9642117.0742   9723475.8742  False
  ACE2   NEO2       230624.2    1.0  -9452172.2742   9913420.6742  False
  ACE2    PBS    229197.4667    1.0  -7676772.7483   8135167.6816  False
  ACE2    REB       -84530.2    1.0  -9767326.6742   9598266.2742  False
  ACE2    SAA      1328987.0    1.0  -8353809.4742  11011783.4742  False
  ACE2  SAC05      -253845.8    1.0  -9936642.2742   9428950.6742  False
  ACE2   SAC2       -19748.6    1.0  -9702545.0742   9663047.8742  False
  ACE2    SOR    640887.7333    1.0  -7265082.4816   8546857.9483  False
  ACE2    STE      -690099.8    1.0 -10372896.2742   8992696.6742  False
  ACE2    SUC       491422.0    1.0  -9191374.4742  10174218.4742  False
  ACE2  THA03       453065.2    1.0  -9229731.2742  10135861.6742  False
  ACE2   THA2       556670.2    1.0  -9126126.2742  10239466.6742  False
  ACE2    XYL      1254932.6    1.0  -8427863.8742  10937729.0742  False
   ADV    ASP       651964.0    1.0  -9030832.4742  10334760.4742  False
   ADV    BAS   -789126.5333    1.0  -8695096.7483   7116843.6816  False
   ADV    CYC       104102.2    1.0  -9578694.2742   9786898.6742  False
   ADV    ERY       895470.2    1.0  -8787326.2742  10578266.6742  False
   ADV    FOS       820458.4    1.0  -8862338.0742  10503254.8742  False
   ADV    GLU      1479226.8    1.0  -8203569.6742  11162023.2742  False
   ADV    HSH     10175592.0 0.0265    492795.5258  19858388.4742   True
   ADV    ISO     27859828.8    0.0  18177032.3258  37542625.2742   True
   ADV    KES       437026.2    1.0  -9245770.2742  10119822.6742  False
   ADV    LAC       -98041.6    1.0  -9780838.0742   9584754.8742  False
   ADV    MAL     34028670.0    0.0  24345873.5258  43711466.4742   True
   ADV    MAN       -43809.8    1.0   -7949780.015    7862160.415  False
   ADV    MFE     -1250290.2    1.0 -10933086.6742   8432506.2742  False
   ADV    NDC      -438069.2    1.0 -10120865.6742   9244727.2742  False
   ADV NEO006      -353646.4    1.0 -10036442.8742   9329150.0742  False
   ADV   NEO2      -163701.6    1.0  -9846498.0742   9519094.8742  False
   ADV    PBS   -165128.3333    1.0  -8071098.5483   7740841.8816  False
   ADV    REB      -478856.0    1.0 -10161652.4742   9203940.4742  False
   ADV    SAA       934661.2    1.0  -8748135.2742  10617457.6742  False
   ADV  SAC05      -648171.6    1.0 -10330968.0742   9034624.8742  False
   ADV   SAC2      -414074.4    1.0 -10096870.8742   9268722.0742  False
   ADV    SOR    246561.9333    1.0  -7659408.2816   8152532.1483  False
   ADV    STE     -1084425.6    1.0 -10767222.0742   8598370.8742  False
   ADV    SUC        97096.2    1.0  -9585700.2742   9779892.6742  False
   ADV  THA03        58739.4    1.0  -9624057.0742   9741535.8742  False
   ADV   THA2       162344.4    1.0  -9520452.0742   9845140.8742  False
   ADV    XYL       860606.8    1.0  -8822189.6742  10543403.2742  False
   ASP    BAS  -1441090.5333    1.0  -9347060.7483   6464879.6816  False
   ASP    CYC      -547861.8    1.0 -10230658.2742   9134934.6742  False
   ASP    ERY       243506.2    1.0  -9439290.2742   9926302.6742  False
   ASP    FOS       168494.4    1.0  -9514302.0742   9851290.8742  False
   ASP    GLU       827262.8    1.0  -8855533.6742  10510059.2742  False
   ASP    HSH      9523628.0 0.0607   -159168.4742  19206424.4742  False
   ASP    ISO     27207864.8    0.0  17525068.3258  36890661.2742   True
   ASP    KES      -214937.8    1.0  -9897734.2742   9467858.6742  False
   ASP    LAC      -750005.6    1.0 -10432802.0742   8932790.8742  False
   ASP    MAL     33376706.0    0.0  23693909.5258  43059502.4742   True
   ASP    MAN      -695773.8    1.0   -8601744.015    7210196.415  False
   ASP    MFE     -1902254.2    1.0 -11585050.6742   7780542.2742  False
   ASP    NDC     -1090033.2    1.0 -10772829.6742   8592763.2742  False
   ASP NEO006     -1005610.4    1.0 -10688406.8742   8677186.0742  False
   ASP   NEO2      -815665.6    1.0 -10498462.0742   8867130.8742  False
   ASP    PBS   -817092.3333    1.0  -8723062.5483   7088877.8816  False
   ASP    REB     -1130820.0    1.0 -10813616.4742   8551976.4742  False
   ASP    SAA       282697.2    1.0  -9400099.2742   9965493.6742  False
   ASP  SAC05     -1300135.6    1.0 -10982932.0742   8382660.8742  False
   ASP   SAC2     -1066038.4    1.0 -10748834.8742   8616758.0742  False
   ASP    SOR   -405402.0667    1.0  -8311372.2816   7500568.1483  False
   ASP    STE     -1736389.6    1.0 -11419186.0742   7946406.8742  False
   ASP    SUC      -554867.8    1.0 -10237664.2742   9127928.6742  False
   ASP  THA03      -593224.6    1.0 -10276021.0742   9089571.8742  False
   ASP   THA2      -489619.6    1.0 -10172416.0742   9193176.8742  False
   ASP    XYL       208642.8    1.0  -9474153.6742   9891439.2742  False
   BAS    CYC    893228.7333    1.0  -7012741.4816   8799198.9483  False
   BAS    ERY   1684596.7333    1.0  -6221373.4816   9590566.9483  False
   BAS    FOS   1609584.9333    1.0  -6296385.2816   9515555.1483  False
   BAS    GLU   2268353.3333    1.0  -5637616.8816  10174323.5483  False
   BAS    HSH  10964718.5333 0.0002   3058748.3184  18870688.7483   True
   BAS    ISO  28648955.3333    0.0  20742985.1184  36554925.5483   True
   BAS    KES   1226152.7333    1.0  -6679817.4816   9132122.9483  False
   BAS    LAC    691084.9333    1.0  -7214885.2816   8597055.1483  False
   BAS    MAL  34817796.5333    0.0  26911826.3184  42723766.7483   True
   BAS    MAN    745316.7333    1.0  -4845048.4175   6335681.8842  False
   BAS    MFE   -461163.6667    1.0  -8367133.8816   7444806.5483  False
   BAS    NDC    351057.3333    1.0  -7554912.8816   8257027.5483  False
   BAS NEO006    435480.1333    1.0  -7470490.0816   8341450.3483  False
   BAS   NEO2    625424.9333    1.0  -7280545.2816   8531395.1483  False
   BAS    PBS       623998.2    1.0  -4966366.9509   6214363.3509  False
   BAS    REB    310270.5333    1.0  -7595699.6816   8216240.7483  False
   BAS    SAA   1723787.7333    1.0  -6182182.4816   9629757.9483  False
   BAS  SAC05    140954.9333    1.0  -7765015.2816   8046925.1483  False
   BAS   SAC2    375052.1333    1.0  -7530918.0816   8281022.3483  False
   BAS    SOR   1035688.4667    1.0  -4554676.6842   6626053.6175  False
   BAS    STE   -295299.0667    1.0  -8201269.2816   7610671.1483  False
   BAS    SUC    886222.7333    1.0  -7019747.4816   8792192.9483  False
   BAS  THA03    847865.9333    1.0  -7058104.2816   8753836.1483  False
   BAS   THA2    951470.9333    1.0  -6954499.2816   8857441.1483  False
   BAS    XYL   1649733.3333    1.0  -6256236.8816   9555703.5483  False
   CYC    ERY       791368.0    1.0  -8891428.4742  10474164.4742  False
   CYC    FOS       716356.2    1.0  -8966440.2742  10399152.6742  False
   CYC    GLU      1375124.6    1.0  -8307671.8742  11057921.0742  False
   CYC    HSH     10071489.8 0.0304    388693.3258  19754286.2742   True
   CYC    ISO     27755726.6    0.0  18072930.1258  37438523.0742   True
   CYC    KES       332924.0    1.0  -9349872.4742  10015720.4742  False
   CYC    LAC      -202143.8    1.0  -9884940.2742   9480652.6742  False
   CYC    MAL     33924567.8    0.0  24241771.3258  43607364.2742   True
   CYC    MAN      -147912.0    1.0   -8053882.215    7758058.215  False
   CYC    MFE     -1354392.4    1.0 -11037188.8742   8328404.0742  False
   CYC    NDC      -542171.4    1.0 -10224967.8742   9140625.0742  False
   CYC NEO006      -457748.6    1.0 -10140545.0742   9225047.8742  False
   CYC   NEO2      -267803.8    1.0  -9950600.2742   9414992.6742  False
   CYC    PBS   -269230.5333    1.0  -8175200.7483   7636739.6816  False
   CYC    REB      -582958.2    1.0 -10265754.6742   9099838.2742  False
   CYC    SAA       830559.0    1.0  -8852237.4742  10513355.4742  False
   CYC  SAC05      -752273.8    1.0 -10435070.2742   8930522.6742  False
   CYC   SAC2      -518176.6    1.0 -10200973.0742   9164619.8742  False
   CYC    SOR    142459.7333    1.0  -7763510.4816   8048429.9483  False
   CYC    STE     -1188527.8    1.0 -10871324.2742   8494268.6742  False
   CYC    SUC        -7006.0    1.0  -9689802.4742   9675790.4742  False
   CYC  THA03       -45362.8    1.0  -9728159.2742   9637433.6742  False
   CYC   THA2        58242.2    1.0  -9624554.2742   9741038.6742  False
   CYC    XYL       756504.6    1.0  -8926291.8742  10439301.0742  False
   ERY    FOS       -75011.8    1.0  -9757808.2742   9607784.6742  False
   ERY    GLU       583756.6    1.0  -9099039.8742  10266553.0742  False
   ERY    HSH      9280121.8  0.081   -402674.6742  18962918.2742  False
   ERY    ISO     26964358.6    0.0  17281562.1258  36647155.0742   True
   ERY    KES      -458444.0    1.0 -10141240.4742   9224352.4742  False
   ERY    LAC      -993511.8    1.0 -10676308.2742   8689284.6742  False
   ERY    MAL     33133199.8    0.0  23450403.3258  42815996.2742   True
   ERY    MAN      -939280.0    1.0   -8845250.215    6966690.215  False
   ERY    MFE     -2145760.4    1.0 -11828556.8742   7537036.0742  False
   ERY    NDC     -1333539.4    1.0 -11016335.8742   8349257.0742  False
   ERY NEO006     -1249116.6    1.0 -10931913.0742   8433679.8742  False
   ERY   NEO2     -1059171.8    1.0 -10741968.2742   8623624.6742  False
   ERY    PBS  -1060598.5333    1.0  -8966568.7483   6845371.6816  False
   ERY    REB     -1374326.2    1.0 -11057122.6742   8308470.2742  False
   ERY    SAA        39191.0    1.0  -9643605.4742   9721987.4742  False
   ERY  SAC05     -1543641.8    1.0 -11226438.2742   8139154.6742  False
   ERY   SAC2     -1309544.6    1.0 -10992341.0742   8373251.8742  False
   ERY    SOR   -648908.2667    1.0  -8554878.4816   7257061.9483  False
   ERY    STE     -1979895.8    1.0 -11662692.2742   7702900.6742  False
   ERY    SUC      -798374.0    1.0 -10481170.4742   8884422.4742  False
   ERY  THA03      -836730.8    1.0 -10519527.2742   8846065.6742  False
   ERY   THA2      -733125.8    1.0 -10415922.2742   8949670.6742  False
   ERY    XYL       -34863.4    1.0  -9717659.8742   9647933.0742  False
   FOS    GLU       658768.4    1.0  -9024028.0742  10341564.8742  False
   FOS    HSH      9355133.6 0.0742   -327662.8742  19037930.0742  False
   FOS    ISO     27039370.4    0.0  17356573.9258  36722166.8742   True
   FOS    KES      -383432.2    1.0 -10066228.6742   9299364.2742  False
   FOS    LAC      -918500.0    1.0 -10601296.4742   8764296.4742  False
   FOS    MAL     33208211.6    0.0  23525415.1258  42891008.0742   True
   FOS    MAN      -864268.2    1.0   -8770238.415    7041702.015  False
   FOS    MFE     -2070748.6    1.0 -11753545.0742   7612047.8742  False
   FOS    NDC     -1258527.6    1.0 -10941324.0742   8424268.8742  False
   FOS NEO006     -1174104.8    1.0 -10856901.2742   8508691.6742  False
   FOS   NEO2      -984160.0    1.0 -10666956.4742   8698636.4742  False
   FOS    PBS   -985586.7333    1.0  -8891556.9483   6920383.4816  False
   FOS    REB     -1299314.4    1.0 -10982110.8742   8383482.0742  False
   FOS    SAA       114202.8    1.0  -9568593.6742   9796999.2742  False
   FOS  SAC05     -1468630.0    1.0 -11151426.4742   8214166.4742  False
   FOS   SAC2     -1234532.8    1.0 -10917329.2742   8448263.6742  False
   FOS    SOR   -573896.4667    1.0  -8479866.6816   7332073.7483  False
   FOS    STE     -1904884.0    1.0 -11587680.4742   7777912.4742  False
   FOS    SUC      -723362.2    1.0 -10406158.6742   8959434.2742  False
   FOS  THA03      -761719.0    1.0 -10444515.4742   8921077.4742  False
   FOS   THA2      -658114.0    1.0 -10340910.4742   9024682.4742  False
   FOS    XYL        40148.4    1.0  -9642648.0742   9722944.8742  False
   GLU    HSH      8696365.2 0.1528   -986431.2742  18379161.6742  False
   GLU    ISO     26380602.0    0.0  16697805.5258  36063398.4742   True
   GLU    KES     -1042200.6    1.0 -10724997.0742   8640595.8742  False
   GLU    LAC     -1577268.4    1.0 -11260064.8742   8105528.0742  False
   GLU    MAL     32549443.2    0.0  22866646.7258  42232239.6742   True
   GLU    MAN     -1523036.6    1.0   -9429006.815    6382933.615  False
   GLU    MFE     -2729517.0    1.0 -12412313.4742   6953279.4742  False
   GLU    NDC     -1917296.0    1.0 -11600092.4742   7765500.4742  False
   GLU NEO006     -1832873.2    1.0 -11515669.6742   7849923.2742  False
   GLU   NEO2     -1642928.4    1.0 -11325724.8742   8039868.0742  False
   GLU    PBS  -1644355.1333    1.0  -9550325.3483   6261615.0816  False
   GLU    REB     -1958082.8    1.0 -11640879.2742   7724713.6742  False
   GLU    SAA      -544565.6    1.0 -10227362.0742   9138230.8742  False
   GLU  SAC05     -2127398.4    1.0 -11810194.8742   7555398.0742  False
   GLU   SAC2     -1893301.2    1.0 -11576097.6742   7789495.2742  False
   GLU    SOR  -1232664.8667    1.0  -9138635.0816   6673305.3483  False
   GLU    STE     -2563652.4    1.0 -12246448.8742   7119144.0742  False
   GLU    SUC     -1382130.6    1.0 -11064927.0742   8300665.8742  False
   GLU  THA03     -1420487.4    1.0 -11103283.8742   8262309.0742  False
   GLU   THA2     -1316882.4    1.0 -10999678.8742   8365914.0742  False
   GLU    XYL      -618620.0    1.0 -10301416.4742   9064176.4742  False
   HSH    ISO     17684236.8    0.0   8001440.3258  27367033.2742   True
   HSH    KES     -9738565.8 0.0466 -19421362.2742    -55769.3258   True
   HSH    LAC    -10273633.6 0.0232 -19956430.0742   -590837.1258   True
   HSH    MAL     23853078.0    0.0  14170281.5258  33535874.4742   True
   HSH    MAN    -10219401.8 0.0008  -18125372.015   -2313431.585   True
   HSH    MFE    -11425882.2 0.0044 -21108678.6742  -1743085.7258   True
   HSH    NDC    -10613661.2 0.0145 -20296457.6742   -930864.7258   True
   HSH NEO006    -10529238.4 0.0163 -20212034.8742   -846441.9258   True
   HSH   NEO2    -10339293.6 0.0213 -20022090.0742   -656497.1258   True
   HSH    PBS -10340720.3333 0.0006 -18246690.5483  -2434750.1184   True
   HSH    REB    -10654448.0 0.0137 -20337244.4742   -971651.5258   True
   HSH    SAA     -9240930.8 0.0847 -18923727.2742    441865.6742  False
   HSH  SAC05    -10823763.6 0.0108 -20506560.0742  -1140967.1258   True
   HSH   SAC2    -10589666.4  0.015 -20272462.8742   -906869.9258   True
   HSH    SOR  -9929030.0667 0.0014 -17835000.2816  -2023059.8517   True
   HSH    STE    -11260017.6 0.0056 -20942814.0742  -1577221.1258   True
   HSH    SUC    -10078495.8 0.0301 -19761292.2742   -395699.3258   True
   HSH  THA03    -10116852.6 0.0287 -19799649.0742   -434056.1258   True
   HSH   THA2    -10013247.6 0.0328 -19696044.0742   -330451.1258   True
   HSH    XYL     -9314985.2 0.0778 -18997781.6742    367811.2742  False
   ISO    KES    -27422802.6    0.0 -37105599.0742 -17740006.1258   True
   ISO    LAC    -27957870.4    0.0 -37640666.8742 -18275073.9258   True
   ISO    MAL      6168841.2 0.8168  -3513955.2742  15851637.6742  False
   ISO    MAN    -27903638.6    0.0  -35809608.815  -19997668.385   True
   ISO    MFE    -29110119.0    0.0 -38792915.4742 -19427322.5258   True
   ISO    NDC    -28297898.0    0.0 -37980694.4742 -18615101.5258   True
   ISO NEO006    -28213475.2    0.0 -37896271.6742 -18530678.7258   True
   ISO   NEO2    -28023530.4    0.0 -37706326.8742 -18340733.9258   True
   ISO    PBS -28024957.1333    0.0 -35930927.3483 -20118986.9184   True
   ISO    REB    -28338684.8    0.0 -38021481.2742 -18655888.3258   True
   ISO    SAA    -26925167.6    0.0 -36607964.0742 -17242371.1258   True
   ISO  SAC05    -28508000.4    0.0 -38190796.8742 -18825203.9258   True
   ISO   SAC2    -28273903.2    0.0 -37956699.6742 -18591106.7258   True
   ISO    SOR -27613266.8667    0.0 -35519237.0816 -19707296.6517   True
   ISO    STE    -28944254.4    0.0 -38627050.8742 -19261457.9258   True
   ISO    SUC    -27762732.6    0.0 -37445529.0742 -18079936.1258   True
   ISO  THA03    -27801089.4    0.0 -37483885.8742 -18118292.9258   True
   ISO   THA2    -27697484.4    0.0 -37380280.8742 -18014687.9258   True
   ISO    XYL    -26999222.0    0.0 -36682018.4742 -17316425.5258   True
   KES    LAC      -535067.8    1.0 -10217864.2742   9147728.6742  False
   KES    MAL     33591643.8    0.0  23908847.3258  43274440.2742   True
   KES    MAN      -480836.0    1.0   -8386806.215    7425134.215  False
   KES    MFE     -1687316.4    1.0 -11370112.8742   7995480.0742  False
   KES    NDC      -875095.4    1.0 -10557891.8742   8807701.0742  False
   KES NEO006      -790672.6    1.0 -10473469.0742   8892123.8742  False
   KES   NEO2      -600727.8    1.0 -10283524.2742   9082068.6742  False
   KES    PBS   -602154.5333    1.0  -8508124.7483   7303815.6816  False
   KES    REB      -915882.2    1.0 -10598678.6742   8766914.2742  False
   KES    SAA       497635.0    1.0  -9185161.4742  10180431.4742  False
   KES  SAC05     -1085197.8    1.0 -10767994.2742   8597598.6742  False
   KES   SAC2      -851100.6    1.0 -10533897.0742   8831695.8742  False
   KES    SOR   -190464.2667    1.0  -8096434.4816   7715505.9483  False
   KES    STE     -1521451.8    1.0 -11204248.2742   8161344.6742  False
   KES    SUC      -339930.0    1.0 -10022726.4742   9342866.4742  False
   KES  THA03      -378286.8    1.0 -10061083.2742   9304509.6742  False
   KES   THA2      -274681.8    1.0  -9957478.2742   9408114.6742  False
   KES    XYL       423580.6    1.0  -9259215.8742  10106377.0742  False
   LAC    MAL     34126711.6    0.0  24443915.1258  43809508.0742   True
   LAC    MAN        54231.8    1.0   -7851738.415    7960202.015  False
   LAC    MFE     -1152248.6    1.0 -10835045.0742   8530547.8742  False
   LAC    NDC      -340027.6    1.0 -10022824.0742   9342768.8742  False
   LAC NEO006      -255604.8    1.0  -9938401.2742   9427191.6742  False
   LAC   NEO2       -65660.0    1.0  -9748456.4742   9617136.4742  False
   LAC    PBS    -67086.7333    1.0  -7973056.9483   7838883.4816  False
   LAC    REB      -380814.4    1.0 -10063610.8742   9301982.0742  False
   LAC    SAA      1032702.8    1.0  -8650093.6742  10715499.2742  False
   LAC  SAC05      -550130.0    1.0 -10232926.4742   9132666.4742  False
   LAC   SAC2      -316032.8    1.0  -9998829.2742   9366763.6742  False
   LAC    SOR    344603.5333    1.0  -7561366.6816   8250573.7483  False
   LAC    STE      -986384.0    1.0 -10669180.4742   8696412.4742  False
   LAC    SUC       195137.8    1.0  -9487658.6742   9877934.2742  False
   LAC  THA03       156781.0    1.0  -9526015.4742   9839577.4742  False
   LAC   THA2       260386.0    1.0  -9422410.4742   9943182.4742  False
   LAC    XYL       958648.4    1.0  -8724148.0742  10641444.8742  False
   MAL    MAN    -34072479.8    0.0  -41978450.015  -26166509.585   True
   MAL    MFE    -35278960.2    0.0 -44961756.6742 -25596163.7258   True
   MAL    NDC    -34466739.2    0.0 -44149535.6742 -24783942.7258   True
   MAL NEO006    -34382316.4    0.0 -44065112.8742 -24699519.9258   True
   MAL   NEO2    -34192371.6    0.0 -43875168.0742 -24509575.1258   True
   MAL    PBS -34193798.3333    0.0 -42099768.5483 -26287828.1184   True
   MAL    REB    -34507526.0    0.0 -44190322.4742 -24824729.5258   True
   MAL    SAA    -33094008.8    0.0 -42776805.2742 -23411212.3258   True
   MAL  SAC05    -34676841.6    0.0 -44359638.0742 -24994045.1258   True
   MAL   SAC2    -34442744.4    0.0 -44125540.8742 -24759947.9258   True
   MAL    SOR -33782108.0667    0.0 -41688078.2816 -25876137.8517   True
   MAL    STE    -35113095.6    0.0 -44795892.0742 -25430299.1258   True
   MAL    SUC    -33931573.8    0.0 -43614370.2742 -24248777.3258   True
   MAL  THA03    -33969930.6    0.0 -43652727.0742 -24287134.1258   True
   MAL   THA2    -33866325.6    0.0 -43549122.0742 -24183529.1258   True
   MAL    XYL    -33168063.2    0.0 -42850859.6742 -23485266.7258   True
   MAN    MFE     -1206480.4    1.0   -9112450.615    6699489.815  False
   MAN    NDC      -394259.4    1.0   -8300229.615    7511710.815  False
   MAN NEO006      -309836.6    1.0   -8215806.815    7596133.615  False
   MAN   NEO2      -119891.8    1.0   -8025862.015    7786078.415  False
   MAN    PBS   -121318.5333    1.0  -5711683.6842   5469046.6175  False
   MAN    REB      -435046.2    1.0   -8341016.415    7470924.015  False
   MAN    SAA       978471.0    1.0   -6927499.215    8884441.215  False
   MAN  SAC05      -604361.8    1.0   -8510332.015    7301608.415  False
   MAN   SAC2      -370264.6    1.0   -8276234.815    7535705.615  False
   MAN    SOR    290371.7333    1.0  -5299993.4175   5880736.8842  False
   MAN    STE     -1040615.8    1.0   -8946586.015    6865354.415  False
   MAN    SUC       140906.0    1.0   -7765064.215    8046876.215  False
   MAN  THA03       102549.2    1.0   -7803421.015    8008519.415  False
   MAN   THA2       206154.2    1.0   -7699816.015    8112124.415  False
   MAN    XYL       904416.6    1.0   -7001553.615    8810386.815  False
   MFE    NDC       812221.0    1.0  -8870575.4742  10495017.4742  False
   MFE NEO006       896643.8    1.0  -8786152.6742  10579440.2742  False
   MFE   NEO2      1086588.6    1.0  -8596207.8742  10769385.0742  False
   MFE    PBS   1085161.8667    1.0  -6820808.3483   8991132.0816  False
   MFE    REB       771434.2    1.0  -8911362.2742  10454230.6742  False
   MFE    SAA      2184951.4    1.0  -7497845.0742  11867747.8742  False
   MFE  SAC05       602118.6    1.0  -9080677.8742  10284915.0742  False
   MFE   SAC2       836215.8    1.0  -8846580.6742  10519012.2742  False
   MFE    SOR   1496852.1333    1.0  -6409118.0816   9402822.3483  False
   MFE    STE       165864.6    1.0  -9516931.8742   9848661.0742  False
   MFE    SUC      1347386.4    1.0  -8335410.0742  11030182.8742  False
   MFE  THA03      1309029.6    1.0  -8373766.8742  10991826.0742  False
   MFE   THA2      1412634.6    1.0  -8270161.8742  11095431.0742  False
   MFE    XYL      2110897.0    1.0  -7571899.4742  11793693.4742  False
   NDC NEO006        84422.8    1.0  -9598373.6742   9767219.2742  False
   NDC   NEO2       274367.6    1.0  -9408428.8742   9957164.0742  False
   NDC    PBS    272940.8667    1.0  -7633029.3483   8178911.0816  False
   NDC    REB       -40786.8    1.0  -9723583.2742   9642009.6742  False
   NDC    SAA      1372730.4    1.0  -8310066.0742  11055526.8742  False
   NDC  SAC05      -210102.4    1.0  -9892898.8742   9472694.0742  False
   NDC   SAC2        23994.8    1.0  -9658801.6742   9706791.2742  False
   NDC    SOR    684631.1333    1.0  -7221339.0816   8590601.3483  False
   NDC    STE      -646356.4    1.0 -10329152.8742   9036440.0742  False
   NDC    SUC       535165.4    1.0  -9147631.0742  10217961.8742  False
   NDC  THA03       496808.6    1.0  -9185987.8742  10179605.0742  False
   NDC   THA2       600413.6    1.0  -9082382.8742  10283210.0742  False
   NDC    XYL      1298676.0    1.0  -8384120.4742  10981472.4742  False
NEO006   NEO2       189944.8    1.0  -9492851.6742   9872741.2742  False
NEO006    PBS    188518.0667    1.0  -7717452.1483   8094488.2816  False
NEO006    REB      -125209.6    1.0  -9808006.0742   9557586.8742  False
NEO006    SAA      1288307.6    1.0  -8394488.8742  10971104.0742  False
NEO006  SAC05      -294525.2    1.0  -9977321.6742   9388271.2742  False
NEO006   SAC2       -60428.0    1.0  -9743224.4742   9622368.4742  False
NEO006    SOR    600208.3333    1.0  -7305761.8816   8506178.5483  False
NEO006    STE      -730779.2    1.0 -10413575.6742   8952017.2742  False
NEO006    SUC       450742.6    1.0  -9232053.8742  10133539.0742  False
NEO006  THA03       412385.8    1.0  -9270410.6742  10095182.2742  False
NEO006   THA2       515990.8    1.0  -9166805.6742  10198787.2742  False
NEO006    XYL      1214253.2    1.0  -8468543.2742  10897049.6742  False
  NEO2    PBS     -1426.7333    1.0  -7907396.9483   7904543.4816  False
  NEO2    REB      -315154.4    1.0  -9997950.8742   9367642.0742  False
  NEO2    SAA      1098362.8    1.0  -8584433.6742  10781159.2742  False
  NEO2  SAC05      -484470.0    1.0 -10167266.4742   9198326.4742  False
  NEO2   SAC2      -250372.8    1.0  -9933169.2742   9432423.6742  False
  NEO2    SOR    410263.5333    1.0  -7495706.6816   8316233.7483  False
  NEO2    STE      -920724.0    1.0 -10603520.4742   8762072.4742  False
  NEO2    SUC       260797.8    1.0  -9421998.6742   9943594.2742  False
  NEO2  THA03       222441.0    1.0  -9460355.4742   9905237.4742  False
  NEO2   THA2       326046.0    1.0  -9356750.4742  10008842.4742  False
  NEO2    XYL      1024308.4    1.0  -8658488.0742  10707104.8742  False
   PBS    REB   -313727.6667    1.0  -8219697.8816   7592242.5483  False
   PBS    SAA   1099789.5333    1.0  -6806180.6816   9005759.7483  False
   PBS  SAC05   -483043.2667    1.0  -8389013.4816   7422926.9483  False
   PBS   SAC2   -248946.0667    1.0  -8154916.2816   7657024.1483  False
   PBS    SOR    411690.2667    1.0  -5178674.8842   6002055.4175  False
   PBS    STE   -919297.2667    1.0  -8825267.4816   6986672.9483  False
   PBS    SUC    262224.5333    1.0  -7643745.6816   8168194.7483  False
   PBS  THA03    223867.7333    1.0  -7682102.4816   8129837.9483  False
   PBS   THA2    327472.7333    1.0  -7578497.4816   8233442.9483  False
   PBS    XYL   1025735.1333    1.0  -6880235.0816   8931705.3483  False
   REB    SAA      1413517.2    1.0  -8269279.2742  11096313.6742  False
   REB  SAC05      -169315.6    1.0  -9852112.0742   9513480.8742  False
   REB   SAC2        64781.6    1.0  -9618014.8742   9747578.0742  False
   REB    SOR    725417.9333    1.0  -7180552.2816   8631388.1483  False
   REB    STE      -605569.6    1.0 -10288366.0742   9077226.8742  False
   REB    SUC       575952.2    1.0  -9106844.2742  10258748.6742  False
   REB  THA03       537595.4    1.0  -9145201.0742  10220391.8742  False
   REB   THA2       641200.4    1.0  -9041596.0742  10323996.8742  False
   REB    XYL      1339462.8    1.0  -8343333.6742  11022259.2742  False
   SAA  SAC05     -1582832.8    1.0 -11265629.2742   8099963.6742  False
   SAA   SAC2     -1348735.6    1.0 -11031532.0742   8334060.8742  False
   SAA    SOR   -688099.2667    1.0  -8594069.4816   7217870.9483  False
   SAA    STE     -2019086.8    1.0 -11701883.2742   7663709.6742  False
   SAA    SUC      -837565.0    1.0 -10520361.4742   8845231.4742  False
   SAA  THA03      -875921.8    1.0 -10558718.2742   8806874.6742  False
   SAA   THA2      -772316.8    1.0 -10455113.2742   8910479.6742  False
   SAA    XYL       -74054.4    1.0  -9756850.8742   9608742.0742  False
 SAC05   SAC2       234097.2    1.0  -9448699.2742   9916893.6742  False
 SAC05    SOR    894733.5333    1.0  -7011236.6816   8800703.7483  False
 SAC05    STE      -436254.0    1.0 -10119050.4742   9246542.4742  False
 SAC05    SUC       745267.8    1.0  -8937528.6742  10428064.2742  False
 SAC05  THA03       706911.0    1.0  -8975885.4742  10389707.4742  False
 SAC05   THA2       810516.0    1.0  -8872280.4742  10493312.4742  False
 SAC05    XYL      1508778.4    1.0  -8174018.0742  11191574.8742  False
  SAC2    SOR    660636.3333    1.0  -7245333.8816   8566606.5483  False
  SAC2    STE      -670351.2    1.0 -10353147.6742   9012445.2742  False
  SAC2    SUC       511170.6    1.0  -9171625.8742  10193967.0742  False
  SAC2  THA03       472813.8    1.0  -9209982.6742  10155610.2742  False
  SAC2   THA2       576418.8    1.0  -9106377.6742  10259215.2742  False
  SAC2    XYL      1274681.2    1.0  -8408115.2742  10957477.6742  False
   SOR    STE  -1330987.5333    1.0  -9236957.7483   6574982.6816  False
   SOR    SUC   -149465.7333    1.0  -8055435.9483   7756504.4816  False
   SOR  THA03   -187822.5333    1.0  -8093792.7483   7718147.6816  False
   SOR   THA2    -84217.5333    1.0  -7990187.7483   7821752.6816  False
   SOR    XYL    614044.8667    1.0  -7291925.3483   8520015.0816  False
   STE    SUC      1181521.8    1.0  -8501274.6742  10864318.2742  False
   STE  THA03      1143165.0    1.0  -8539631.4742  10825961.4742  False
   STE   THA2      1246770.0    1.0  -8436026.4742  10929566.4742  False
   STE    XYL      1945032.4    1.0  -7737764.0742  11627828.8742  False
   SUC  THA03       -38356.8    1.0  -9721153.2742   9644439.6742  False
   SUC   THA2        65248.2    1.0  -9617548.2742   9748044.6742  False
   SUC    XYL       763510.6    1.0  -8919285.8742  10446307.0742  False
 THA03   THA2       103605.0    1.0  -9579191.4742   9786401.4742  False
 THA03    XYL       801867.4    1.0  -8880929.0742  10484663.8742  False
  THA2    XYL       698262.4    1.0  -8984534.0742  10381058.8742  False
------------------------------------------------------------------------
  • plot tukey result
In [ ]:
tp = TukeyPlot()
tp.plot_tukey(df_tukey)
Out[ ]:
<Axes: title={'center': 'The Tukey test result'}, xlabel='The difference of mean value', ylabel='Groups'>

3.3 T-Test¶

  • Select the two groups of interest for the T-test
In [ ]:
df_ttest = sw.get_stats_ttest(group_list=['MAL', 'PBS'])
display(df_ttest.sort_values(by='P-value'))

t-test for Taxon-Description in ['MAL', 'PBS']

100%|██████████| 20739/20739 [00:33<00:00, 614.41it/s]
P-value t-statistic V1_32 V2_32 V3_32 V4_32 V5_32 V1_01 V1_26 V1_37 ... V2_37 V3_01 V3_26 V3_37 V4_01 V4_26 V4_37 V5_01 V5_26 V5_37
Taxon Description
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A Belongs to the bacterial ribosomal protein bS16 family 6.530428e-11 13.604118 3405147 2031408 3890510 3174528 3735839 495699 618303 0 ... 0 0 606541 0 377076 0 0 0 408600 0
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A massiliensis Belongs to the phosphoglycerate kinase family 1.422027e-10 12.974279 10544927 7925416 12979505 8669368 10268308 2376259 2298544 2032377 ... 3021435 2468879 2453278 1687110 3090003 1835245 3525475 2499385 1936377 1649894
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A Putative cell wall binding repeat 5.536336e-10 11.931107 4024996 2184018 2897185 3198223 3172044 467096 0 290105 ... 364883 606735 0 618545 244241 441393 63637 481833 142226 870203
Bacterial extracellular solute-binding protein 6.026885e-10 11.868243 55357633 38368403 69739326 37982563 64018487 10357237 5822630 9279453 ... 9029598 10329806 12966514 9913544 5018059 3957163 2260259 7135096 5804131 9991801
Psort location Cytoplasmic, score 9.98 8.880045e-09 10.003715 33008066 62835342 53925379 41611821 70276260 16946312 16233511 10743316 ... 13545490 15380275 11562475 13704287 16578006 8585544 11287176 15287787 16077613 12603490
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila_A Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin NaN NaN 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp004167605 Glycoside hydrolase, family 20, catalytic core NaN NaN 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
May play a key role in the regulation of the intracellular concentration of adenosylhomocysteine NaN NaN 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp900766865 Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome NaN NaN 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
Pyruvate phosphate dikinase, PEP/pyruvate binding domain NaN NaN 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0

20739 rows × 22 columns

  • Plot top 100 taxa-function across heatmap (p-value)
In [ ]:
hp.plot_top_taxa_func_heatmap_of_test_res(df_ttest, sw.func, 100, 'p')

Table size: 20739 x 22
Recommended figure size: width: 27, length: 40, front_title: 20, font_size: 10
Out[ ]:
<seaborn.matrix.ClusterGrid at 0x187829e3e20>

3.4 DESeq2 for Log2FC¶

  • Select the two groups of interest for calculating log2FC
In [ ]:
df_fc = sw.get_stats_deseq2(sw.taxa_func_df , group_list=['MAL', 'PBS'])

Fitting size factors...
... done in 0.02 seconds.

Fitting dispersions...
... done in 3.63 seconds.

Fitting dispersion trend curve...
... done in 5.58 seconds.

Fitting MAP dispersions...
... done in 3.45 seconds.

Fitting LFCs...
... done in 8.65 seconds.

Refitting 5499 outliers.

Fitting dispersions...
... done in 0.69 seconds.

Fitting MAP dispersions...
... done in 0.59 seconds.

Fitting LFCs...
... done in 4.27 seconds.

Running Wald tests...
... done in 1.52 seconds.

Log2 fold change & Wald test p-value: Sweetener PBS vs MAL
baseMean log2FoldChange lfcSE stat pvalue padj
Taxa-Func
d__Archaea|p__Halobacteriota|c__Halobacteria|o__Halobacteriales|f__Haloferacaceae|g__Haloferax|s__Haloferax massiliensis [Electron transfer flavoprotein, beta subunit] 0.000000 NaN NaN NaN NaN NaN
d__Archaea|p__Halobacteriota|c__Halobacteria|o__Halobacteriales|f__Haloferacaceae|g__Haloferax|s__Haloferax massiliensis [Involved in regulation of DNA replication] 7328.721114 -0.337907 2.304200 -0.146648 0.883410 0.999902
d__Archaea|p__Halobacteriota|c__Halobacteria|o__Halobacteriales|f__Haloferacaceae|g__Haloferax|s__Haloferax massiliensis [NADH ubiquinone oxidoreductase subunit 1 (Chain H)] 0.000000 NaN NaN NaN NaN NaN
d__Archaea|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobacterium|s__Methanobacterium sp000499765 [Binds directly to 23S rRNA. Probably involved in E site tRNA release] 4244.426286 -4.409273 3.331767 -1.323403 NaN NaN
d__Archaea|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobacterium|s__Methanobacterium sp000499765 [Molecular chaperone capable of stabilizing a range of proteins. Seems to fulfill an ATP-independent, HSP70-like function in archaeal de novo protein folding] 0.000000 NaN NaN NaN NaN NaN
... ... ... ... ... ... ...
d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp004167605 [Prevents misfolding and promotes the refolding and proper assembly of unfolded polypeptides generated under stress conditions] 6156.085578 0.017438 0.963073 0.018107 0.985554 0.999902
d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp004167605 [carbohydrate kinase activity] 2124.127616 -0.167809 2.660427 -0.063076 0.949706 0.999902
d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp004167605 [outer membrane autotransporter barrel domain protein] 162.398547 8.914786 0.000000 0.000000 NaN NaN
d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp900766865 [Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome] 0.000000 NaN NaN NaN NaN NaN
d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp900766865 [Pyruvate phosphate dikinase, PEP/pyruvate binding domain] 0.000000 NaN NaN NaN NaN NaN

20739 rows × 6 columns

  • Show the DESeq2 result table sorted by padj and log2FoldChange
In [ ]:
display(df_fc.sort_values(by=['padj', 'log2FoldChange']))
baseMean log2FoldChange lfcSE stat pvalue padj V1_32 V2_32 V3_32 V4_32 ... V2_37 V3_01 V3_26 V3_37 V4_01 V4_26 V4_37 V5_01 V5_26 V5_37
Taxa-Func
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [Alpha amylase catalytic] 125962.524088 -3.348493 0.379603 -8.821037 1.134047e-18 1.579274e-14 20316636 27951767 45648544 28992727 ... 3550704 5603981 5221565 6940798 4124013 2674402 4526463 2119099 2277697 2426268
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [Psort location Cytoplasmic, score 9.98] 233511.214560 -1.973048 0.257091 -7.674504 1.660605e-14 1.156279e-10 33008066 62835342 53925379 41611821 ... 13545490 15380275 11562475 13704287 16578006 8585544 11287176 15287787 16077613 12603490
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [D-isomer specific 2-hydroxyacid dehydrogenase] 1918.011025 -15.361539 2.024428 -7.588090 3.246559e-14 1.507052e-10 1264470 157859 523497 219077 ... 0 0 0 0 0 0 0 0 0 0
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [Bacterial extracellular solute-binding protein] 194107.642804 -2.768583 0.369716 -7.488398 6.971951e-14 2.427285e-10 55357633 38368403 69739326 37982563 ... 9029598 10329806 12966514 9913544 5018059 3957163 2260259 7135096 5804131 9991801
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit] 38199.451975 -2.881334 0.401324 -7.179569 6.993161e-13 1.725167e-09 7711614 6443415 12765501 8050715 ... 1319253 1887998 1882542 1700035 1292280 1040357 328831 1746933 2588074 1509087
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila_A [Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin] 0.000000 NaN NaN NaN NaN NaN 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp004167605 [Glycoside hydrolase, family 20, catalytic core] 0.000000 NaN NaN NaN NaN NaN 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp004167605 [May play a key role in the regulation of the intracellular concentration of adenosylhomocysteine] 0.000000 NaN NaN NaN NaN NaN 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp900766865 [Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome] 0.000000 NaN NaN NaN NaN NaN 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp900766865 [Pyruvate phosphate dikinase, PEP/pyruvate binding domain] 0.000000 NaN NaN NaN NaN NaN 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0

20739 rows × 26 columns

  • Volcano plot with padj=0.05, log2fc=1
In [ ]:
vp = VolcanoPlot()
vp.plot_volcano(df = df_fc, padj=0.05, log2fc=1, title_name='NDC vs BAS', figsize=(8, 6))
Out[ ]:
<Axes: title={'center': 'Volcano plot of NDC vs BAS (padj < 0.05, log2FoldChange > 1)'}, xlabel='log2FoldChange', ylabel='-log10(padj)'>
  • Sankey plot withwidth=1200, height=800, p_value=0.005, log2fc=1
In [ ]:
sp = SankeyPlot()
pic = sp.plot_fc_sankey(df_fc, width=1200, height=800, p_value=0.005, log2fc=1)
pic.render_notebook()

Creating nodes and links for upregulated...
Number of nodes: 101
Number of links: 102
Creating nodes and links for downregulated...
Number of nodes: 70
Number of links: 69
Out[ ]:

4. Other functions¶

4.1 Get some basic info¶

  • Input: a group name
  • output: a list containing all samples of the group
In [ ]:
sw.get_sample_list_in_a_group('NDC')
Out[ ]:
['V1_17', 'V2_17', 'V3_17', 'V4_17', 'V5_17']
  • Input: a meat name
  • output: a list containing all groups of the meta
In [ ]:
print(sw.get_meta_list('Person'))

['V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5']

4.2 Get intensity matrix¶

In [ ]:
taxon = 'd__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A'
function = 'Alpha amylase catalytic'
  • Input: a taxon name
  • output: A matrix of all functional intensity under the taxon
In [ ]:
sw.get_intensity_matrix(taxon_name=taxon)
Out[ ]:
V1_01 V1_02 V1_03 V1_04 V1_05 V1_06 V1_07 V1_08 V1_09 V1_10 ... V5_29 V5_30 V5_31 V5_32 V5_33 V5_34 V5_35 V5_36 V5_37 V5_38
Description
4Fe-4S dicluster domain 0 2615194 862507 0 1657281 0 0 202091 0 306054 ... 0 0 4359213 3974126 7630749 0 0 0 0 2036744
ABC transporter substrate binding protein 399325 0 0 554314 0 0 0 276083 454484 282606 ... 279801 241201 0 232880 0 0 354653 166981 203408 181204
ABC transporter substrate-binding protein PnrA-like 4801530 8214579 6014136 2932604 8927618 5693465 2612510 6079875 3840413 7112622 ... 4873780 2538617 6119082 10595852 8602937 4140661 2924249 3492467 1995332 6695263
ABC transporter, solute-binding protein 68697 1926695 538352 782061 707150 558362 927291 159072 2955851 894248 ... 5423611 0 0 0 491801 0 0 0 0 0
ABC-type branched-chain amino acid transport systems periplasmic component 142014 388602 0 0 233492 0 0 107147 0 0 ... 0 0 151530 0 0 440469 0 0 0 0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
phenylalanyl-tRNA synthetase (beta subunit) 558425 2291605 1047544 622633 2117798 215328 201782 444547 531796 1047894 ... 603772 579479 2748865 4276744 3160508 222057 411237 0 737657 1135023
precorrin-4 C11-methyltransferase 614252 772312 0 1342845 725014 580376 0 846369 1547419 0 ... 0 0 0 1481962 1017100 0 0 0 0 0
self proteolysis 7835853 3782073 2542271 6115328 5946785 5431637 2889251 3079824 3154294 7071532 ... 2908560 5384647 22813316 29091793 15613756 4346420 3843680 2131130 3034220 22607359
translation elongation factor G 3437430 22621869 8663979 1737353 8453812 2728469 2370272 5187042 3487809 5787783 ... 2689900 2391601 7891932 17890371 18866048 1862133 1987872 2038818 2275986 9101159
transport systems ATPase components 573759 502586 328627 216013 853016 0 0 340364 244512 459331 ... 0 1030323 313082 517430 933291 0 559629 550918 313763 0

231 rows × 190 columns

  • Input: a function name
  • output: A matrix of all species intensity under the function
In [ ]:
sw.get_intensity_matrix(func_name=function)
Out[ ]:
V1_01 V1_02 V1_03 V1_04 V1_05 V1_06 V1_07 V1_08 V1_09 V1_10 ... V5_29 V5_30 V5_31 V5_32 V5_33 V5_34 V5_35 V5_36 V5_37 V5_38
Taxon
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A luti 0 1695192 0 0 1625777 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A sp003477525 619484 2817471 710294 504574 2518867 462228 538816 302569 341525 600846 ... 255284 0 0 3601729 0 104086 0 0 0 0
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A 3571092 15314463 4256180 3090474 14250829 3958464 2138617 5030109 3282561 3785770 ... 5417808 1477560 5192762 67409590 6813235 3972182 2838313 3006783 2426268 3675044

3 rows × 190 columns

  • Input: a taxon name and function name
  • output: A matrix of all peptides intensity under the taxa-func
In [ ]:
sw.get_intensity_matrix(taxon_name=taxon, func_name=function)
Out[ ]:
V1_01 V1_02 V1_03 V1_04 V1_05 V1_06 V1_07 V1_08 V1_09 V1_10 ... V5_29 V5_30 V5_31 V5_32 V5_33 V5_34 V5_35 V5_36 V5_37 V5_38
Sequence
ALNNADTITVGEC(Carbamidomethyl)SGVTLEEAKK 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 1315398 0 0 0 0 0 0
ALPMHDYEPDREDGLC(Carbamidomethyl)SIR 0 618606 0 0 385705 0 0 138603 0 137204 ... 0 0 0 1422385 376129 0 152559 108580 0 0
DQINREDSVFK 260958 354036 0 0 825274 362460 0 130755 0 158060 ... 502495 0 158184 6929513 0 230961 258840 168180 0 0
EGELPTNWR 372353 2665658 759794 520188 2560633 680107 0 867148 336808 567680 ... 627490 0 388002 5300408 922208 521595 244269 305343 0 503723
IMMDLVVNHTSDEHK 0 412916 1035354 613620 943625 0 383944 762730 538389 496835 ... 639038 0 881517 2511732 319958 352913 364939 138788 0 1202804
INAKDQINREDSVFK 505599 714323 830983 782399 722507 868311 763122 426687 716517 580215 ... 0 0 0 2478282 0 0 0 0 0 0
KSTDNPYR 309908 602749 0 296602 514596 289842 231717 164608 0 259714 ... 0 0 0 809794 0 0 0 0 0 137398
MQWTDGENAGFTTGKPWLK 376350 1181448 0 0 944313 0 0 0 0 0 ... 355923 0 0 1704527 258665 0 0 0 0 0
MTEEDMMAAIGYK 0 435420 0 0 626554 0 0 0 0 0 ... 526201 0 285410 7823039 440872 339267 0 289379 0 0
SFC(Carbamidomethyl)DSN(Deamidated)GDGIGDLN(Deamidated)GITGK 0 248153 0 0 0 0 0 0 0 0 ... 0 0 0 1117332 0 0 0 0 0 0
SFC(Carbamidomethyl)DSN(Deamidated)GDGIGDLNGITGK 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 2134871 0 0 0 0 0 0
SFC(Carbamidomethyl)DSNGDGIGDLN(Deamidated)GITGK 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 2355751 0 0 0 0 0 0
SFC(Carbamidomethyl)DSNGDGIGDLNGITGK 0 648961 0 0 484536 0 0 0 0 0 ... 0 0 0 3987066 0 0 0 0 0 511658
TLLVVGNYQKEPQTIELAGEC(Carbamidomethyl)R 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
TPMQWTDGENAGFTTGKPWLK 378120 558761 0 287484 474311 0 429778 0 0 0 ... 0 0 0 995511 430143 0 130989 0 0 0
VLISNYI(Xle->Ser)DAK 688196 4111870 391997 0 3039805 874560 0 872370 442626 579671 ... 493869 423337 594338 9593719 665149 597041 690946 559485 398924 540997
VLISNYIDAK 0 0 461146 0 646190 0 0 492259 0 0 ... 1412480 873030 821886 13582660 987505 916913 995771 688161 680664 778464
VNANYTK 679608 2761562 776906 590181 2082780 883184 330056 1174949 1248221 1006391 ... 860312 181193 2063425 3347602 2412606 1013492 0 748867 1346680 0

18 rows × 190 columns

  • Output only the groups we care about
In [ ]:
sw.get_intensity_matrix(taxon_name=taxon, func_name=function, groups=['MAL', 'PBS'])
Out[ ]:
V1_32 V2_32 V3_32 V4_32 V5_32 V1_01 V1_26 V1_37 V2_01 V2_26 V2_37 V3_01 V3_26 V3_37 V4_01 V4_26 V4_37 V5_01 V5_26 V5_37
Sequence
ALNNADTITVGEC(Carbamidomethyl)SGVTLEEAKK 434741 417616 1387643 695346 1315398 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ALPMHDYEPDREDGLC(Carbamidomethyl)SIR 337218 609524 832618 612271 1422385 0 203204 0 0 129616 0 0 0 0 0 0 0 0 0 0
DQINREDSVFK 981283 0 2455104 1620138 6929513 260958 144356 0 0 0 443562 0 0 0 0 0 0 185677 227617 0
EGELPTNWR 3160785 1456018 4665067 3019300 5300408 372353 728259 0 0 0 0 662900 0 462996 636790 0 469682 0 319528 0
IMMDLVVNHTSDEHK 1278639 1278804 1871439 1295025 2511732 0 883181 891795 644631 0 651423 325094 697803 1021961 571719 778144 988552 0 0 0
INAKDQINREDSVFK 945226 480514 667388 735779 2478282 505599 544242 962968 371219 479039 576014 1042643 428329 1027263 0 0 0 0 0 0
KSTDNPYR 616553 1196118 744606 346441 809794 309908 179245 264785 0 0 0 0 118177 0 0 0 0 0 0 0
MQWTDGENAGFTTGKPWLK 863779 601707 1544428 1251519 1704527 376350 291765 0 272426 0 0 436508 273029 448206 0 444139 438718 0 326660 0
MTEEDMMAAIGYK 636212 3450194 2791486 2246693 7823039 0 0 0 494686 526644 371563 407551 389946 611135 320991 0 390194 490641 0 0
SFC(Carbamidomethyl)DSN(Deamidated)GDGIGDLN(Deamidated)GITGK 475946 1018241 677051 0 1117332 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
SFC(Carbamidomethyl)DSN(Deamidated)GDGIGDLNGITGK 832444 1000680 1273125 931489 2134871 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
SFC(Carbamidomethyl)DSNGDGIGDLN(Deamidated)GITGK 666817 1009803 1126245 1114940 2355751 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
SFC(Carbamidomethyl)DSNGDGIGDLNGITGK 492400 1021262 1058611 2188407 3987066 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
TLLVVGNYQKEPQTIELAGEC(Carbamidomethyl)R 0 667588 894714 681946 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
TPMQWTDGENAGFTTGKPWLK 0 518267 1062874 374322 995511 378120 0 0 0 0 0 0 0 0 339144 0 0 0 0 0
VLISNYI(Xle->Ser)DAK 4384464 9780422 17734368 4625617 9593719 688196 398316 452609 648577 727875 0 1364226 1217237 959671 958381 782352 905763 569983 352194 398924
VLISNYIDAK 1859258 848574 307211 4400783 13582660 0 401518 0 911352 613049 743575 481944 810339 571172 527753 356389 380404 581342 736870 680664
VNANYTK 2350871 2596435 4554566 2852711 3347602 679608 647583 805761 631602 764432 764567 883115 1286705 1838394 769235 313378 953150 291456 314828 1346680

4.3 Get top intensity matrix of test results ('anova', 'ttest' or 'log2fc')¶

  • Top 10 intensity matrix of T-test results
In [ ]:
sw.get_top_intensity_matrix_of_test_res(df_ttest, df_type='ttest', top_num=10)
Out[ ]:
V1_32 V2_32 V3_32 V4_32 V5_32 V1_01 V1_26 V1_37 V2_01 V2_26 V2_37 V3_01 V3_26 V3_37 V4_01 V4_26 V4_37 V5_01 V5_26 V5_37
Taxa-Func
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [Belongs to the bacterial ribosomal protein bS16 family] 3405147 2031408 3890510 3174528 3735839 495699 618303 0 547513 660347 0 0 606541 0 377076 0 0 0 408600 0
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A massiliensis [Belongs to the phosphoglycerate kinase family] 10544927 7925416 12979505 8669368 10268308 2376259 2298544 2032377 3984972 3559154 3021435 2468879 2453278 1687110 3090003 1835245 3525475 2499385 1936377 1649894
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [Putative cell wall binding repeat] 4024996 2184018 2897185 3198223 3172044 467096 0 290105 1289805 271961 364883 606735 0 618545 244241 441393 63637 481833 142226 870203
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [Bacterial extracellular solute-binding protein] 55357633 38368403 69739326 37982563 64018487 10357237 5822630 9279453 9944561 10069509 9029598 10329806 12966514 9913544 5018059 3957163 2260259 7135096 5804131 9991801
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [Psort location Cytoplasmic, score 9.98] 33008066 62835342 53925379 41611821 70276260 16946312 16233511 10743316 14235220 11635923 13545490 15380275 11562475 13704287 16578006 8585544 11287176 15287787 16077613 12603490
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [Psort location CytoplasmicMembrane, score 9.75] 673700 922783 865928 576781 1037950 467309 194477 78400 0 0 122718 243406 0 0 0 0 0 0 0 0
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A sp003477525 [Alpha amylase catalytic] 3287917 2910844 5938048 2417397 3601729 619484 255115 374653 666260 497054 748190 262388 333507 271965 152341 165736 0 0 0 0
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [Catalyzes the conversion of N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) to 4-carboxy-5-aminoimidazole ribonucleotide (CAIR)] 2012315 2331128 4225992 4520725 5936002 383915 0 0 0 0 0 417303 373176 0 0 0 156443 0 0 0
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [Plays an important role in the de novo pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP] 6624441 5728486 13980073 7957624 12377792 818545 1213816 792025 1109360 839295 961701 1488777 1909321 1141391 1507205 314757 738168 1112445 0 0
d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [Converts alpha-aldose to the beta-anomer] 2979891 2552639 5769546 2785415 6061225 573312 81611 410258 319646 203478 144851 88940 122465 0 54850 0 0 312584 215240 108597

4.4 Plot intensity heatmap¶

  • Plot a intensity heatmap of a function
  • All sample names are automatically added to the grouping information in parentheses
  • Different colors represent different groups
In [ ]:
hp.plot_basic_heatmap(mat=sw.get_intensity_matrix(func_name=function), title='Alpha amylase catalytic')

Table size: 3 x 190
Recommended figure size: width: 40, length: 12, front_title: 20, font_size: 10
Out[ ]:
<seaborn.matrix.ClusterGrid at 0x187a1f0c5b0>
<Figure size 4000x1200 with 0 Axes>
  • Plot a intensity heatmap of a taxa-func
In [ ]:
hp.plot_basic_heatmap(mat=sw.get_intensity_matrix(taxon_name=taxon,func_name=function ), title='Intensity of Blautia_A wexlerae_A - Alpha amylase catalytic')

Table size: 18 x 190
Recommended figure size: width: 40, length: 14.0, front_title: 20, font_size: 10
Out[ ]:
<seaborn.matrix.ClusterGrid at 0x1879c039880>
<Figure size 4000x1400 with 0 Axes>
  • Plot a intensity heatmap of a function of some groups we care
In [ ]:
hp.plot_basic_heatmap(mat=sw.get_intensity_matrix(func_name=function, groups=['MAL', 'PBS'] ), title='Alpha amylase catalytic')

Table size: 3 x 20
Recommended figure size: width: 25, length: 12, front_title: 15, font_size: 10
Out[ ]:
<seaborn.matrix.ClusterGrid at 0x1879fb66070>
<Figure size 2500x1200 with 0 Axes>
  • Plot a intensity heatmap of a taxa-func of some groups
In [ ]:
hp.plot_basic_heatmap(mat=sw.get_intensity_matrix(taxon_name=taxon,func_name=function, groups=['MAL', 'PBS'] ), title='Intensity of Blautia_A wexlerae_A - Alpha amylase catalytic')

Table size: 18 x 20
Recommended figure size: width: 25, length: 14.0, front_title: 15, font_size: 10
Out[ ]:
<seaborn.matrix.ClusterGrid at 0x1879fcc79a0>
<Figure size 2500x1400 with 0 Axes>

4.5 Line plot of intensity¶

  • plot line of intensity of different samples
In [ ]:
lp = LinePlot(sw)
lp.plot_intensity_line(func_name=function, fig_size=(25, 10))
Out[ ]:
<Axes: title={'center': 'Alpha amylase catalytic'}, xlabel='Samples', ylabel='Intensity'>
In [ ]:
lp.plot_intensity_line(taxon_name=taxon,func_name=function, fig_size=(25,10))
Out[ ]:
<Axes: title={'center': 'd__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A\nAlpha amylase catalytic'}, xlabel='Samples', ylabel='Intensity'>